At least a million children at 8,000 schools will be barred from lessons today as striking teachers trigger acute shortages across the country.

Headteachers and teaching assistants have been drafted in to take the place of striking colleagues after school authorities failed to avert widespread school closures. A third of schools will be turning some pupils away and one in six will close entirely.

Over 100,000 civil servants - from driving test supervisors to coastguards - and 30,000 college lecturers are also walking out in the biggest strike over pay since Labour came to power.

Ministers, opposition MPs and other teaching unions all accused the National Union of Teachers of jeopardising children's education and teachers' reputations. The action is expected to cost the economy millions of pounds in lost working days as some parents are forced to take time off.

A survey of every local authority conducted jointly by the Local Government Association and the Guardian reveals:

· In 102 of the 188 local authorities in England and Wales, 2,086 schools will definitely close with 2,229 reporting partial closures.

· Only one of the 102 authorities reported that no schools would close. If the pattern is repeated in all authorities, up to 8,000 schools will be affected - nearly a third across England and Wales.

· Large rural authorities with lots of small primary schools have been most vulnerable. In Norfolk 189 schools are closing or partially closing, in Cumbria 142 and in Essex 122. Nottinghamshire has 106 schools affected and Cheshire has 98.

Secondaries have been able to prevent more closures by sending home older children and focusing their non-striking members of staff on keeping younger children in schools to minimise the impact on children and their parents.

Members of the NUT, which is Europe's largest teaching union, are protesting about a 2.45% pay deal which they say will leave teachers worse off because of the rising cost of living. Schools will face teacher shortages unless wages, particularly for the youngest teachers struggling to get on the housing ladder, are made competitive with other graduate professions, they say.

Jim Knight, the schools minister, told the Guardian: "I share parents' frustrations. People are bewildered by this action. The average salary is now £34,000 and has gone up by 19% in real terms in the past ten years.

"It is a real concern that the rising reputation of teachers will be damaged by this action. The public find it difficult to understand why teachers are doing this. We're pretty sure the majority of schools will be unaffected tomorrow. But it is very frustrating that some teachers are taking this industrial action."

Nick Gibb, the Conservative shadow schools minister, said: "It is deeply regrettable that so many children will have their education disrupted by this strike, especially as the pay deal was recommended by an independent panel and accepted by the other teaching unions. Many children have important exams coming up soon and can't afford to miss crucial lessons, and many parents will have to miss work to look after them."

David Laws, the Liberal Democrat education spokesman, said: "I am concerned that it will damage the education of children at a key time of the year, inconvenience many parents and undermine the image of the teaching profession."

Christine Blower, acting general secretary of the NUT, said: "Teachers do not take the decision to strike easily, or lightly, but teachers' patience has been stretched to the limit. This is not just a one-year issue. After three years of below inflation pay increases the prospect for a further three years of the same is the last straw. The Retail Price Index, which features on government websites as the figure used for pay bargaining, is currently running at a yearly average of 4.1%. The current pay offer of 2.45% is well below that and can be seen in no other way than as a pay cut.

"Year on year pay that fails to keep pace with inflation has real consequences for the profession and schools. It saps morale and causes problems of recruitment, retention and teacher shortages, not to mention real financial difficulty for members. It is time to call a halt. Real term pay cuts hit youngest teachers the hardest."

More than 100,000 civil servants and nearly 30,000 lecturers in 250 colleges are also walking out today in a coordinated "day of discontent" in protest against Gordon Brown's 2% pay freeze.

Coastguard workers walked out last night in their third 24-hour stoppage and this morning are due to be joined by benefit office staff, immigration officers, passport office staff at Heathrow terminal 5, Gatwick, Stansted and Dover and land registry officials. Local government workers in the Unison union in Birmingham are also expected to join the strike. Joint rallies are planned around the country.

The children's secretary, Ed Balls, is also under further pressure after being accused of putting plans for a diploma at risk by splitting the government departments responsible for its delivery.

A report from the children, schools and families select committee accuses Balls' Children's Plan of lacking a "mission".

The plan sets 10 targets for 2020, including to introduce a new measure of children's wellbeing, improve skills at the start of primary and secondary school, reduce obesity, eradicate child poverty and "significantly reduce" the number of children convicted of criminal offences.

"The Children's Plan runs the risk of being simply a wish list rather than the mission for the department," says the committee report.